Abstract

Background

Pigs are well known source of human infectious disease. To better understand the spectrum
of viruses present in pigs, we utilized the 454 Life Sciences GS-FLX high-throughput
sequencing platform to sequence stool samples from healthy pigs.

Findings

Total nucleic acid was extracted from stool samples of healthy piglets and randomly
amplified. The amplified materials were pooled and processed using a high-throughput
pyrosequencing technique. The raw sequences were deconvoluted on the basis of the
barcode and then processed through a standardized bioinformatics pipeline. The unique
reads (348, 70 and 13) had limited similarity to known astroviruses, bocaviruses and
parechoviruses. Specific primers were synthesized to assess the prevalence of the
viruses in healthy piglets. Our results indicate extremely high rates of positivity.

Conclusions

Several novel astroviruses, bocaviruses and Ljungan-like viruses were identified in
stool samples from healthy pigs. The rates of isolation for the new viruses were high.
The high detection rate, diverse sequences and categories indicate that pigs are well-established
reservoirs for and likely sources of different enteric viruses.